Mercurial > repos > engineson > multiqc
changeset 14:784165ccd3c1 draft
Uploaded
| author | engineson |
|---|---|
| date | Fri, 07 Jul 2017 08:00:39 -0400 |
| parents | e17597fc06fb |
| children | d6579f50e622 |
| files | readme.rst |
| diffstat | 1 files changed, 533 insertions(+), 24 deletions(-) [+] |
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--- a/readme.rst Fri Jul 07 07:57:43 2017 -0400 +++ b/readme.rst Fri Jul 07 08:00:39 2017 -0400 @@ -1,36 +1,545 @@ -======================== -Galaxy multiqc wrapper -======================== + + + + + + +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <link rel="dns-prefetch" href="https://assets-cdn.github.com"> + <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> + <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> + <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> + + + + <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-e04a23d39bf81b7db3c635177756ef51bc171feb440be9e174933c6eb56382da.css" media="all" rel="stylesheet" /> + <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-caabe7e9677dbaa4c88db92fcc52ed61b0def1a9d2e3d3ab196c0a5c81d20d04.css" media="all" rel="stylesheet" /> + + + <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/site-4ff621027ab732d24efccdbfda10b40d3be645de22ff72aeccd01041076ef761.css" media="all" rel="stylesheet" /> + + + <meta name="viewport" content="width=device-width"> + + <title>galaxy_tools/readme.rst at master · EnginesOn/galaxy_tools · GitHub</title> + <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> + <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> + <meta property="fb:app_id" content="1401488693436528"> + + + <meta content="https://avatars1.githubusercontent.com/u/18550486?v=3&s=400" property="og:image" /><meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="EnginesOn/galaxy_tools" property="og:title" /><meta content="https://github.com/EnginesOn/galaxy_tools" property="og:url" /><meta content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization" property="og:description" /> + + <link rel="assets" href="https://assets-cdn.github.com/"> + + <meta name="pjax-timeout" content="1000"> + + <meta name="request-id" content="8872:424F:107FF96:1C0B105:595F77E6" data-pjax-transient> + + + <meta name="selected-link" value="repo_source" data-pjax-transient> + + <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> +<meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> + <meta name="google-analytics" content="UA-3769691-2"> + +<meta content="collector.githubapp.com" name="octolytics-host" /><meta content="github" name="octolytics-app-id" /><meta content="https://collector.githubapp.com/github-external/browser_event" name="octolytics-event-url" /><meta content="8872:424F:107FF96:1C0B105:595F77E6" name="octolytics-dimension-request_id" /><meta content="iad" name="octolytics-dimension-region_edge" /><meta content="iad" name="octolytics-dimension-region_render" /> +<meta content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" name="analytics-location" /> + + + + + <meta class="js-ga-set" name="dimension1" content="Logged Out"> + + + + + <meta name="hostname" content="github.com"> + <meta name="user-login" content=""> + + <meta name="expected-hostname" content="github.com"> + <meta name="js-proxy-site-detection-payload" content="NDk4NWM3NGQ5NWRkMjc1NDdjOWYxNGM0NDQzYjQzN2RlNjY1OTE4ZDVhZmFiM2M5ZjA4MjRiOThiNDM5ZTRmZHx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI4ODcyOjQyNEY6MTA3RkY5NjoxQzBCMTA1OjU5NUY3N0U2IiwidGltZXN0YW1wIjoxNDk5NDI4ODM5LCJob3N0IjoiZ2l0aHViLmNvbSJ9"> + -Aggregate results from bioinformatics analyses across many samples into a single report + <meta name="html-safe-nonce" content="f994e8c4f0b29df4becc5beba1587922214b447d"> + + <meta http-equiv="x-pjax-version" content="f47291fda1809c6a5b3a2f5f4848063e"> + + + <link href="https://github.com/EnginesOn/galaxy_tools/commits/master.atom" rel="alternate" title="Recent Commits to galaxy_tools:master" type="application/atom+xml"> + + <meta name="description" content="galaxy_tools - 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name="user-content-galaxy-multiqc-wrapper"></a> +<h2><a id="user-content-galaxy-multiqc-wrapper" class="anchor" href="#galaxy-multiqc-wrapper" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Galaxy multiqc wrapper</h2> +<p>Aggregate results from bioinformatics analyses across many samples into a single report</p> +<p>MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.</p> +<a name="user-content-installation"></a> +<h2><a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Installation</h2> +<p>Requirements: pkg-config</p> +<p>Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory.</p> +<a name="user-content-prevent-displaying-multiqc-webpage-as-gibberish"></a> +<h2><a id="user-content-prevent-displaying-multiqc-webpage-as-gibberish" class="anchor" href="#prevent-displaying-multiqc-webpage-as-gibberish" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Prevent displaying MultiQC webpage as gibberish</h2> +<p>For Galaxy to display MultiQC's HTML output properly, you need to either:</p> +<ol> +<li>Deactivate the sanitize_all_html option in galaxy.ini (sanitize_all_html = False), or</li> +<li>Whitelist the tool in "Manage Display Whitelist" after installing</li> +</ol> +<a name="user-content-history"></a> +<h2><a id="user-content-history" class="anchor" href="#history" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>History</h2> +<blockquote> +<ul> +<li>v1.0.0.0 Update to multiQC 1.0, add additional supported tools</li> +<li>v0.6: Initial public release</li> +</ul> +</blockquote> +<a name="user-content-citation"></a> +<h2><a id="user-content-citation" 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